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74 changes: 74 additions & 0 deletions
74
backend/src/main/kotlin/org/loculus/backend/utils/EarliestReleaseDateFinder.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| package org.loculus.backend.utils | ||
|
|
||
| import kotlinx.datetime.LocalDate | ||
| import kotlinx.datetime.LocalDateTime | ||
| import kotlinx.datetime.LocalTime | ||
| import mu.KotlinLogging | ||
| import org.loculus.backend.service.submission.RawProcessedData | ||
|
|
||
| private val log = KotlinLogging.logger { } | ||
|
|
||
| /** | ||
| * Calculate the earliest release date for rows of sequence entries given to it one by one. | ||
| * Assumes that rows are sorted: all accession entries are given in a block, and with ascending versions. | ||
| * | ||
| * The earliest release date of a sequence is the earliest date of: | ||
| * - the internal release date | ||
| * - any date from a given list of fields | ||
| * - the earliest release date from the previous version (if it exists) | ||
| */ | ||
| class EarliestReleaseDateFinder(private val fields: List<String>) { | ||
| private val earliestReleaseDateCache = mutableMapOf<String, LocalDateTime>() | ||
| private var previousRawProcessedData: RawProcessedData? = null | ||
|
|
||
| fun calculateEarliestReleaseDate(rawProcessedData: RawProcessedData): LocalDateTime { | ||
| assert( | ||
| previousRawProcessedData == null || | ||
| rawProcessedData.accession > previousRawProcessedData!!.accession || | ||
| ( | ||
| rawProcessedData.accession == previousRawProcessedData!!.accession && | ||
| rawProcessedData.version > previousRawProcessedData!!.version | ||
| ), | ||
| ) { | ||
| "Input is not ordered. Current: ${rawProcessedData.accession}.${rawProcessedData.version}, " + | ||
| "Previous: ${previousRawProcessedData!!.accession}.${previousRawProcessedData!!.version}" | ||
| } | ||
|
|
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| var earliestReleaseDate = rawProcessedData.releasedAtTimestamp | ||
|
|
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| fields.forEach { field -> | ||
| rawProcessedData.processedData.metadata[field]?.textValue()?.let { dateText -> | ||
| val date = try { | ||
| LocalDateTime(LocalDate.parse(dateText), LocalTime.fromSecondOfDay(0)) | ||
| } catch (e: IllegalArgumentException) { | ||
| log.error { | ||
| "Unexpected error: Incorrectly formatted date on ${rawProcessedData.accession}." + | ||
| "${rawProcessedData.version} on field $field: $dateText " + | ||
| "Something is wrong with this instance: it might be a configuration error or a bug of " + | ||
| "the software. Please feel free to reach out to the developers if you need advice " + | ||
| "(https://github.com/loculus-project/loculus/issues/)." | ||
| } | ||
| null | ||
| } | ||
| if (date != null) { | ||
| earliestReleaseDate = if (date < earliestReleaseDate) date else earliestReleaseDate | ||
| } | ||
| } | ||
| } | ||
|
|
||
| earliestReleaseDateCache[rawProcessedData.accession]?.let { cached -> | ||
| if (cached < earliestReleaseDate) { | ||
| earliestReleaseDate = cached | ||
| } else { | ||
| earliestReleaseDateCache[rawProcessedData.accession] = earliestReleaseDate | ||
| } | ||
| } ?: run { | ||
| earliestReleaseDateCache.clear() // Inputs are ordered; no need for previous values | ||
| earliestReleaseDateCache[rawProcessedData.accession] = earliestReleaseDate | ||
| } | ||
|
|
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| previousRawProcessedData = rawProcessedData | ||
|
|
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| return earliestReleaseDate | ||
| } | ||
| } |
74 changes: 74 additions & 0 deletions
74
backend/src/test/kotlin/org/loculus/backend/config/BackendSpringConfigTest.kt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| package org.loculus.backend.config | ||
|
|
||
| import org.hamcrest.MatcherAssert.assertThat | ||
| import org.hamcrest.Matchers.`is` | ||
| import org.junit.jupiter.api.Assertions.assertTrue | ||
| import org.junit.jupiter.api.Test | ||
| import org.loculus.backend.controller.DEFAULT_ORGANISM | ||
|
|
||
| class BackendSpringConfigTest { | ||
|
|
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| @Test | ||
| fun `GIVEN an empty config THEN the it is valid`() { | ||
| val conf = backendConfig(emptyList(), EarliestReleaseDate(false, emptyList())) | ||
|
|
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| val errors = validateEarliestReleaseDateFields(conf) | ||
|
|
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| assertTrue(errors.isEmpty()) | ||
| } | ||
|
|
||
| @Test | ||
| fun `GIVEN a config with earliestReleaseDate configured with existing date fields THEN it is valid`() { | ||
| val conf = backendConfig( | ||
| listOf( | ||
| Metadata("foo", MetadataType.DATE), | ||
| Metadata("bar", MetadataType.DATE), | ||
| ), | ||
| EarliestReleaseDate(true, listOf("foo", "bar")), | ||
| ) | ||
|
|
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| val errors = validateEarliestReleaseDateFields(conf) | ||
|
|
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| assertTrue(errors.isEmpty()) | ||
| } | ||
|
|
||
| @Test | ||
| fun `GIVEN a config with a missing external field in earliestReleaseDate THEN it is invalid`() { | ||
| val conf = backendConfig( | ||
| listOf( | ||
| Metadata("foo", MetadataType.DATE), | ||
| ), | ||
| EarliestReleaseDate(true, listOf("foo", "bar")), | ||
| ) | ||
|
|
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| val errors = validateEarliestReleaseDateFields(conf) | ||
|
|
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| assertThat(errors.size, `is`(1)) | ||
| } | ||
|
|
||
| @Test | ||
| fun `GIVEN a config with an external field with incorrect type in earliestReleaseDate THEN it is invalid`() { | ||
| val conf = backendConfig( | ||
| listOf( | ||
| Metadata("foo", MetadataType.DATE), | ||
| Metadata("bar", MetadataType.STRING), | ||
| ), | ||
| EarliestReleaseDate(true, listOf("foo", "bar")), | ||
| ) | ||
|
|
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| val errors = validateEarliestReleaseDateFields(conf) | ||
|
|
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| assertThat(errors.size, `is`(1)) | ||
| } | ||
| } | ||
|
|
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| fun backendConfig(metadataList: List<Metadata>, earliestReleaseDate: EarliestReleaseDate) = BackendConfig( | ||
| organisms = mapOf( | ||
| DEFAULT_ORGANISM to InstanceConfig( | ||
| Schema(DEFAULT_ORGANISM, metadataList, earliestReleaseDate = earliestReleaseDate), | ||
| ReferenceGenome(emptyList(), emptyList()), | ||
| ), | ||
| ), | ||
| accessionPrefix = "FOO_", | ||
| dataUseTermsUrls = null, | ||
| ) |
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